[2024-01-25 20:19:35,693] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:35,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:35,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg244da9c6-7bbc-446f-84eb-314722a04939/dqc_reference
[2024-01-25 20:19:36,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:36,793] [INFO] Task started: Prodigal
[2024-01-25 20:19:36,794] [INFO] Running command: gunzip -c /var/lib/cwl/stg114363e4-d9ee-4bea-a82c-4f5043d1a524/GCF_015352955.1_ASM1535295v1_genomic.fna.gz | prodigal -d GCF_015352955.1_ASM1535295v1_genomic.fna/cds.fna -a GCF_015352955.1_ASM1535295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:52,174] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:52,174] [INFO] Task started: HMMsearch
[2024-01-25 20:19:52,174] [INFO] Running command: hmmsearch --tblout GCF_015352955.1_ASM1535295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg244da9c6-7bbc-446f-84eb-314722a04939/dqc_reference/reference_markers.hmm GCF_015352955.1_ASM1535295v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:52,436] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:52,437] [INFO] Found 6/6 markers.
[2024-01-25 20:19:52,482] [INFO] Query marker FASTA was written to GCF_015352955.1_ASM1535295v1_genomic.fna/markers.fasta
[2024-01-25 20:19:52,482] [INFO] Task started: Blastn
[2024-01-25 20:19:52,482] [INFO] Running command: blastn -query GCF_015352955.1_ASM1535295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg244da9c6-7bbc-446f-84eb-314722a04939/dqc_reference/reference_markers.fasta -out GCF_015352955.1_ASM1535295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:53,421] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:53,424] [INFO] Selected 25 target genomes.
[2024-01-25 20:19:53,424] [INFO] Target genome list was writen to GCF_015352955.1_ASM1535295v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:53,430] [INFO] Task started: fastANI
[2024-01-25 20:19:53,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg114363e4-d9ee-4bea-a82c-4f5043d1a524/GCF_015352955.1_ASM1535295v1_genomic.fna.gz --refList GCF_015352955.1_ASM1535295v1_genomic.fna/target_genomes.txt --output GCF_015352955.1_ASM1535295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:19,383] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:19,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg244da9c6-7bbc-446f-84eb-314722a04939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:19,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg244da9c6-7bbc-446f-84eb-314722a04939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:19,400] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:20:19,400] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:20:19,401] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	81.4248	909	1817	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	80.8873	724	1817	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	80.4194	650	1817	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	80.1178	638	1817	95	below_threshold
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	80.0354	475	1817	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	79.8936	669	1817	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	79.7046	563	1817	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	79.7039	562	1817	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	79.612	565	1817	95	below_threshold
Herbaspirillum chlorophenolicum	strain=NBRC 102525	GCA_001571165.1	211589	211589	type	True	79.5991	547	1817	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	79.5943	561	1817	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	79.5435	680	1817	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	79.5209	562	1817	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	79.5163	582	1817	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.4835	451	1817	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	79.4709	626	1817	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	79.3467	521	1817	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	79.3144	509	1817	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	79.2732	683	1817	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	79.2443	583	1817	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	79.2133	596	1817	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	79.2042	442	1817	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	79.101	506	1817	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	79.0766	619	1817	95	below_threshold
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	79.0754	608	1817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:19,402] [INFO] DFAST Taxonomy check result was written to GCF_015352955.1_ASM1535295v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:19,402] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:19,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:19,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg244da9c6-7bbc-446f-84eb-314722a04939/dqc_reference/checkm_data
[2024-01-25 20:20:19,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:19,456] [INFO] Task started: CheckM
[2024-01-25 20:20:19,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015352955.1_ASM1535295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015352955.1_ASM1535295v1_genomic.fna/checkm_input GCF_015352955.1_ASM1535295v1_genomic.fna/checkm_result
[2024-01-25 20:21:06,843] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:06,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:06,868] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:06,868] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:06,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015352955.1_ASM1535295v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:06,869] [INFO] Task started: Blastn
[2024-01-25 20:21:06,869] [INFO] Running command: blastn -query GCF_015352955.1_ASM1535295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg244da9c6-7bbc-446f-84eb-314722a04939/dqc_reference/reference_markers_gtdb.fasta -out GCF_015352955.1_ASM1535295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:08,843] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:08,848] [INFO] Selected 19 target genomes.
[2024-01-25 20:21:08,848] [INFO] Target genome list was writen to GCF_015352955.1_ASM1535295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:08,879] [INFO] Task started: fastANI
[2024-01-25 20:21:08,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg114363e4-d9ee-4bea-a82c-4f5043d1a524/GCF_015352955.1_ASM1535295v1_genomic.fna.gz --refList GCF_015352955.1_ASM1535295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015352955.1_ASM1535295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:30,165] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:30,177] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:30,177] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_015352955.1	s__Noviherbaspirillum_A soli	100.0	1813	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019052805.1	s__Noviherbaspirillum_A sp019052805	91.1621	1415	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016632335.1	s__Noviherbaspirillum_A pedocola	81.4023	912	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188095.1	s__Noviherbaspirillum humi	80.8857	724	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744395.1	s__Herbaspirillum sp017744395	80.3528	579	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715495.1	s__Herbaspirillum sp006715495	80.2319	584	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	99.71	99.15	0.99	0.96	4	-
GCF_002213415.1	s__Herbaspirillum robiniae	80.1195	639	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	80.0932	537	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	80.0912	716	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635065.1	s__Oxalicibacterium flavum	80.0751	471	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590835.1	s__Paucimonas sp003590835	79.8366	518	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	79.7263	369	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016429215.1	s__Herbaspirillum sp016429215	79.6983	544	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213425.1	s__Herbaspirillum aquaticum	79.6199	564	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.01	95.53	0.89	0.85	3	-
GCF_000221045.1	s__Collimonas fungivorans_A	79.5178	498	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCF_018304945.1	s__Collimonas sp018304945	79.3435	519	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	-
GCF_014635845.1	s__Oxalicibacterium solurbis	79.1892	443	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408245.1	s__Duganella sp013408245	79.1771	628	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	79.1011	505	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:30,180] [INFO] GTDB search result was written to GCF_015352955.1_ASM1535295v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:30,180] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:30,184] [INFO] DFAST_QC result json was written to GCF_015352955.1_ASM1535295v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:30,184] [INFO] DFAST_QC completed!
[2024-01-25 20:21:30,184] [INFO] Total running time: 0h1m54s